Crystal structure of Pim1 kinase in complex with inhibitor (Z)-2-[(1H-indazol-3-yl)methylene]-6-methoxy-7-(piperazin-1-ylmethyl)benzofuran-3(2H)-one

Experimental Data Snapshot

  • Resolution: 2.08 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

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Rational evolution of a novel type of potent and selective proviral integration site in Moloney murine leukemia virus kinase 1 (PIM1) inhibitor from a screening-hit compound.

Nakano, H.Saito, N.Parker, L.J.Tada, Y.Abe, M.Tsuganezawa, K.Yokoyama, S.Tanaka, A.Kojima, H.Okabe, T.Nagano, T.

(2012) J Med Chem 55: 5151-5164

  • DOI: https://doi.org/10.1021/jm3001289
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Serine/threonine kinase PIM1 is an emerging therapeutic target for hematopoietic and prostate cancer therapy. To develop a novel PIM1 inhibitor, we focused on 1, a metabolically labile, nonselective kinase inhibitor discovered in our previous screening study. We adopted a rational optimization strategy based mainly on structural information for the PIM1-1 complex to improve the potency and selectivity. This approach afforded the potent and metabolically stable PIM1-selective inhibitor 14, which shows only a marginal increase in molecular weight compared with 1 but has a significantly decreased cLogP. The validity of our design concept was confirmed by X-ray structure analysis. In a cellular study, 14 potently inhibited the growth of human leukemia cell line MV4-11 but had a negligible effect on the growth of WI-38 (surrogate for general toxicity). These results demonstrate the effectiveness of our design strategy for evolving the screening-hit compound 1 into a novel type of PIM1 inhibitor, 14.

  • Organizational Affiliation

    Open Innovation Center for Drug Discovery, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proto-oncogene serine/threonine-protein kinase pim-1298Homo sapiensMutation(s): 0 
Gene Names: pim1
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
PHAROS:  P11309
GTEx:  ENSG00000137193 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11309
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 596

Download Ideal Coordinates CCD File 
D [auth A](2Z)-2-(1H-indazol-3-ylmethylidene)-6-methoxy-7-(piperazin-1-ylmethyl)-1-benzofuran-3(2H)-one
C22 H22 N4 O3
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
596 PDBBind:  3UMW IC50: 3 (nM) from 1 assay(s)
BindingDB:  3UMW IC50: min: 3, max: 6 (nM) from 2 assay(s)
Binding MOAD:  3UMW IC50: 3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.08 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.28α = 90
b = 98.28β = 90
c = 80.641γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
MOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description